FSL

FSL is a comprehensive library of analysis tools for FMRI, MRI and diffusion brain imaging data FSL is installed in /usr/local/fsl and activated for all users by default.

Setup FSL

You need to set the FSLDIR environment variable to point to the FSL installation directory before you can run anything:

# FSL Setup
FSLDIR=/usr/local/fsl
PATH=${FSLDIR}/share/fsl/bin:${PATH}
export FSLDIR PATH
. ${FSLDIR}/etc/fslconf/fsl.sh

Further documentation

For more information on how to use FSL, you should read the FSL documentation.